The fitness cost of antibiotic resistance in the absence of antibiotics is crucial to the success of suspending antibiotics as a strategy to lower resistance. Here we show that after antibiotic treatment the cost of resistance within the complex ecosystem of the mammalian gut is personalized. Using mice as an in vivo model, we find that the fitness effect of the same resistant mutation can be deleterious in a host, but neutral or even beneficial in other hosts. Such antagonistic pleiotropy is shaped by the microbiota, as in germ-free mice resistance is consistently costly across all hosts. An eco-evolutionary model of competition for resources identifies a general mechanism underlying between host variation and predicts that the dynamics of compensatory evolution of resistant bacteria should be host specific, a prediction that was supported by experimental evolution in vivo. The microbiome of each human is close to unique and our results suggest that the short-term costs of resistance and its long-term withinhost evolution will also be highly personalized, a finding that may contribute to the observed variable outcome of control therapies.

ABSTRACT. Acinetobacter sp isolates deserve special attention once they have emerged globally in healthcare institutions because they display numerous intrinsic and acquired drug-resistance mechanisms. This study assessed the antibiotic susceptibility profile, the presence of the genetic marker bla , and the clonal relationship among 34 nosocomial isolates of Acinetobacter spp obtained at a hospital in southeastern Brazil. Antibiotic sensitivity analysis was performed by the standard disc-diffusion method. All isolates were found to be extensively resistant to several drugs, but sensitive to polymyxin B. A polymerase chain reaction (PCR) assay was used to detect the bla OXA-23 gene, which is associated with carbapenem resistance. The genetic profile and the clonal relationship among isolates were analyzed via enterobacterial repetitive intergenic consensus (ERIC)-PCR. The Acinetobacter spp were divided into four groups with 22 distinct genetic subgroups. ERIC-PCR analysis revealed the genetic diversity among isolates, which, despite having a heterogeneous profile, displayed 100% clonality among 56% (19/34) of them.

We characterized six drug-resistant nosocomial isolates of Klebsiella pneumoniae obtained in a hospital located in northern Minas Gerais State, Brazil, by determining their antibiotic sensitivity profiles, detecting the bla KPC genetic marker and examining their clonal relationships. All isolates were found to be extensively drug resistant. A PCR assay was used to confirm the identity of the isolates as K. pneumoniae and assess the bla KPC gene. All isolates tested positive for the bla KPC gene, which is related to carbapenem resistance. The genetic profiles and clonal relationships among the isolates were evaluated by ERIC-PCR. All the isolates were in a single group with two distinct subgroups. Analysis of the ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 18 (1): gmr18172 E.R. Lima et al. 2 genetic diversity among the isolates revealed that five of the six were clones, which suggests cross-transmission in this hospital environment. Five of the patients died from infection. We describe the first detection of KPC-producing K. pneumoniae isolates from a hospital in northern Minas Gerais state.

10The fitness cost of antibiotic resistance in the absence of antibiotics is crucial to the 11 success of suspending antibiotics as a strategy to lower resistance. Here we show that 12 after antibiotic treatment the cost of resistance within the complex ecosystem of the 13 mammalian gut is personalized. Using mice as an in vivo model, we find that the 14 fitness effect of the same resistant mutation can be deleterious in a host, but neutral or 15 even beneficial in other hosts. Such antagonistic pleiotropy is shaped by the 16 microbiota, as in germ-free mice resistance is consistently costly across all hosts. An 17 eco-evolutionary model of competition for resources identifies a general mechanism 18 underlying between host variation and predicts that the dynamics of compensatory 19 evolution of resistant bacteria should be host specific, a prediction that was supported 20 by experimental evolution in vivo. The microbiome of each human is close to unique 21 and our results suggest that the short-term costs of resistance and its long-term within-22 host evolution will also be highly personalized, a finding that may contribute to the 23 observed variable outcome of control therapies. 24 25 few studies where pathogens 25-31 were tested during in vivo colonization and infection 51suggest that fitness costs of AR are not always high in the context of bacterial 52 colonization or virulence. Yet to the best of our knowledge, no study so far has 53 analyzed the temporal dynamics of resistant strains colonizing the key ecosystem of 54 the gut microbiota. In particular, it is currently unclear how the results from in vitro 55 studies or in the context of invasive pathogens are informative about AR in gut 56 commensal strains, which are by far the main colonizers of a natural complex 57 ecosystem. Here, we performed in vivo competitive fitness assays, mathematical 58 modeling and in vivo experimental evolution to unravel the fitness effects of AR in 59 commensal E. coli colonizing its natural environment. 60 61 RESULTS 62Competitive fitness of AR in the mouse gut 63We focused on common resistance mutations to streptomycin -Str R (rpsL K43T ) and 64 rifampicin-Rif R (rpoB H526Y ), and also studied double resistant clones -Str R Rif R 65 (rpsL K43T rpoB H526Y ). These have been identified in many important pathogens, such 66as Mycobacterium tuberculosis and Salmonella, and also in pathogenic and 67 commensal E. coli [32][33][34] . 68To query how inter-species interactions, present in the natural ecosystem comprising 69 the mammalian gut, influence the costs of AR, we performed competitive fitness 70 assays in mice that have a complex microbiota (SPF mice). To mimic conditions 71where the rise of AR can occur, mice were given an antibiotic treatment -72 streptomycin -for a week (see Fig. 1a and Methods). Such treatment is known to 73 cause perturbations in the microbiota species composition and also to break 74 colonization resistant to E. coli 35 , thus increasing the probability that colonization by 75